And another one …

I encountered yet another instance of a species that had dropped out of the collective consciousness of biologists last week, with some help from colleagues Lydia King and Luc Ector.   I co-ordinate an exercise whereby all those of us who analyse diatoms regularly for ecological assessments in the UK and Ireland calibrate themselves against one another. The last sample that we used for this exercise came from a small stream in County Tyrone, Northern Ireland, and it contained a mess of Fragilaria species that proved to be rather challenging. Some we could name quite easily, others took a little more work.   Amongst these Fragilaria species was a nice population of Fragilaria vaucheriae, with its distinct one-sided central area, linear-lanceolate outlines and coarse striae. This was close in all respects to the type description, and presented us with few challenges.

115011_Fragilaria_vaucheria

Fragilaria vaucheriae from Trillick Tributary, Carran Bridge, County Tyrone, Northern Ireland, May 2014. Scale bar: 10 micrometres (1/100th of a millimetre). Photographs: Lydia King.

However, there was also a number of valves in the sample which were similar in many respects to the description of F. vaucheriae in the standard floras, but was slightly narrower and which had a more lanceolate outline.   Confusingly, a very similar diatom is illustrated in the 1991 edition of the bwasserflora von Mitteleuropa as one of a number of illustrations of “Fragilaria capucina var. vaucheriae”.   Our sample, however, had two distinct populations: the broader valves which correspond to “true” F. vaucheriae and the narrower ones that many of us, using the bwasserflora, have “lumped” into F. vaucheriae simply because there were no more plausible alternatives on offer.

Luc Ector eventually pointed us towards descriptions and illustrations of another species, Fragilaria pectinalis, which does look very similar to Lydia’s photographs.   Our only slight concern is that the stria density in our population is slightly lower than in the description of the type population of F. pectinalis.   For this reason, we are referring to our population as “Fragilaria cf. pectinalis”, until we are more certain.

115011_Fragilaria_pectinali

Fragilaria cf. pectinalis from Trillick Tributary, Carran Bridge, County Tyrone, Northern Ireland, May 2014. Scale bar: 10 micrometres (1/100th of a millimetre). Photographs: Lydia King.

Fragilaria pectinalis is an interesting case study in the rise and fall of species names.   This species is the type species for the genus Fragilaria, meaning that it was the first species in the genus to be formally described (by Lyngbye in 1819).   It was known from even earlier, albeit under a different name, Conferva pectinalis, although the earliest illustrations are very schematic and hard to interpret.   What is interesting is how it disappeared from Floras and identification guides throughout the 20th century. It is not in Hustedt’s first edition of the bwasserflora von Mitteleuropa, nor is it in West and Fritsch’s Treatise on British Freshwater Algae (1927), Patrick and Reimer’s Diatoms of the United States (1966) or the second edition of the bwasserflora, as I have already mentioned. I suspect that it has generally been lumped into Fragilaria vaucheriae for most of this time. It is only thanks to the detective work of Akihiro Tuji and David Williams that has managed to bring the name back into circulation.

The next step, I guess, is to get it into the standard identification literature again.   My experience is that busy ecologists often do not have the time to trawl through the vast and rather dispersed primary literature every time they encounter a form that they do not recognise.   Hence they exhibit a tendency to squeeze forms into the closest category in the books that they do have.   Luc Ector has started the wheels rolling by including it into his recent publication but perhaps we’ll also see it in the next edition of Diatomeen im Süßwasser-Benthos?  

References

Bey, M.-Y. & Ector, L. (2013). Atlas des diatomées des cours d’eau de la région Rhône-Alpes. Direction régionale de l’Environnement, de l’Aménagement et du Logement Rhône-Alpes. http://www.rhone-alpes.developpement-durable.gouv.fr.

Hofmann, G., Werum, M. & Lange-Bertalot, H. (2011). Diatomeen im Süßwasser-Benthos von Mitteleuropa. A.R.G. Gantner Verlag K.G., Rugell.

Tuji, A. & Williams, D.M. (2006b). Typification of Conferva pectinalis O. F. Müll. (Bacillariophyceae) and the identity of the type of an alleged synonym, Fragilaria capucina Desm.   Taxon 55: 193-199.

Tuji, A. & Williams, D.M. (2008). Examination of types in the Fragilaria pectinalis – capitellata species complex.   Pp. 125-139. In: Proceedings of the Nineteenth International Diatom Symposium 2006 (edited by Y. Likhoshway).   Biopress, Bristol.

 

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Something else we forgot to remember …

The story of the mysterious red alga that I wrote about a couple of weeks ago (see “More than just an insignificant dot?”) has taken another intriguing turn.   Having decided that the alga was probably Audouinella pygmaea, I was shown a paper from 2011 by Orlando Necchi and Marianna Oliveira in which they consider the affinities of Audouinella species and came to the conclusion that Audouinella pygmaea only really exists in the imaginations of people who write identification guides. I’ve written before about the complicated life history of red algae (see “The schizophrenic life of red algae …”) and commented that it can be hard to differentiate between simple red algae such as Audouinella and stages in the life history of more complicated red algae.

Audouinella hermanii, the red alga that I was writing about in those earlier posts, does not present us with any serious problems, as it is possible to see all the reproductive structures, which enables us to distinguish between the (haploid) gametophyte filaments and the (diploid) sporophytes. However, reproductive organs have not been observed on populations of A. pygmaea, which presents us with some problems. Is this really an independent species of Audouinella or just a “chantransia” (gametophyte) stage of another red alga? Necchi and Oliveria took a number of populations of A. pygmaea and another species, A. macrospora (which has not been recorded from Britain or Ireland) and compared their genetic composition with other freshwater algae. What they found was that these chantransia stages were more closely related to known species from other red algal genera than they were to each other.   Their conclusion: “Audouinella pygmaea” does not exist in any meaningful sense. Rather, the populations we describe as A. pygmaea represent life history stages of other red algae. These life history stages are impossible to tell apart from one another using morphological criteria.   However, there is a good chance that a thorough search of the Anghidi Fawr stream upstream of where the sonde was placed will reveal another red alga – most likely Batrachospermum or Thorea – that was releasing the carpospores that produced the filaments that we named Audouinella pygmaea.

Curiously, this brings us back close to the situation almost 100 years ago as, reading my trusty old copy of West and Fritsch I read that the freshwater species we now call Audouinella were then placed in the genus Chantransia and that “C. pygmaea is probably a stage in the life-history of Batrachospermum moniliforme Roth.”   Another case, perhaps, of things we forgot to remember?

Reference

Neechi, O. Jr. & Oliveira, M.C. (2011). Phylogenetic affinities of “chantransia” stages in members of the Batrachospermales and Thoreales (Rhodophyta). Journal of Phycology 47: 680-686.

West, G.S. & Fritsch F.E. (1927). A Treatise on the British Freshwater Algae.   Cambridge University Press, Cambridge.

Hilda Canter-Lund Shortlist 2015 now online

shortlist_combined

The shortlist for the 2015 Hilda Canter-Lund competition is now online at http://www.brphycsoc.org/Canter-Lund_2015/index.lasso. We have a particularly fine shortlist this year, encompassing the wide range of algal diversity from microscopic freshwater plankton to submerged seaweed forests.   Two of the photographers, Chris Carter and John Huisman, are old friends of the competition, both having won it in the past, but they are facing stiff competition from five new faces.

Publication of our shortlist coincides with the shortlist appearing for the biennial Royal Microscopical Society’s Scientific Imaging Competition and I was pleased to see how well our own shortlist stood up to this competition. Their remit is much wider than ours, and some of the images are quite stunning. However, the images picked out for the BBC website showed a distinct predilection for false-coloured SEM images. It may be a personal bias but I generally find the use of false colour to be brash and distracting. When we are putting together the shortlist for the Hilda Canter-Lund competition we are looking for a basic authenticity and honesty in the way that the natural world is presented to the viewer, and this generally precludes excessive use of PhotoShop. Having said that, this year’s shortlist does include one image (“Viral attack”) where sensitive use of false colour does enhance the image and highlights an important role of viruses in oceanic carbon cycling.

The winner will be announced in mid-August.

What’s in a name?

I’ve been thinking a lot recently about how the data ecologists collect moves through organisations and influences the decision-making process (see the chain of three posts starting with “The human ecosystem of environmental management“). And I’ve returned to that subject whilst preparing for a workshop in Cardiff where we are starting to put together an online Flora of the freshwater diatoms of Britain and Ireland. The project is being co-ordinated by Ingrid Jüttner of the National Museum of Wales, with financial support from the British Phycological Society.   It is a big task, because so many new species of diatom have been described over the past twenty years or so, and many existing species have been shuffled into different genera. The current situation is, frankly, bewildering for the frontline ecologists who have to analyse samples from around the country as part of ongoing assessments of river health.

The problem I’ve been addressing in my posts could be summarised as the ecology of information. An ecologist stands in a stream or (more likely) sits in a laboratory processing samples. S/he finds a preponderance of organisms that are indicative of a polluted river. How does that observation then move through the organisation and influence a decision on the management of that river?   My earlier posts considered this in very general terms; now I want to look in more detail at the issues concerning recording biological data, because the first step a frontline biologist takes after completing a survey or analysing a sample is to add the results to a computer database. But this is where the complications start.

Most of the identification literature written before about 1990 included a common species called Synedra ulna.   Since this time, however, there has been a dispute about the correct name of this species (summarised in the paper referenced below).   The widespread view now is that the correct name (albeit based on a rather pedantic interpretation of the International Code of Botanical Nomenclature) is Ulnaria ulna.   The species is the same; only the name has changed. This debate was continuing as we put together the current UK assessment tool, DARLEQ, and we adopted a conservative position, sticking with the name Synedra ulna.

This means that the software associated with this tool, and the underlying databases operated by the environmental agencies, all included the name ‘Synedra ulna’ but not the name ‘Ulnaria ulna’. Fast forward a few years to our new diatom Flora where we follow current practice and use the name Ulnaria ulna. Analysts who use our Flora will then record this name, not Synedra ulna, in their notebooks but then run into a problem when they want to add this name to the database, because it is not in the list of names that they are offered.

This is one of the points where the practice of an academic researcher and a biologist in a large organisation such as the Environment Agency diverges. Like many researchers, I have a database where I store my records but this is a low-key affair that is stored on my desktop. It is easy for me to open the file where I store the name of species and add one or two more each time there is a change in our understanding. When a single database serves a large organisation with legal responsibilities, the system has to be very secure and protected against well-meaning individuals tinkering with the mechanisms. That makes it harder to keep up-to-date with taxonomic and nomenclatural changes; more so when budgets have been slashed across the public services.

The problem is further compounded because biologists have to download data from the main database (“BIOSYS”, in the case of the Environment Agency) in order to load it into the standalone package, “DARLEQ”, that calculates the diatom indices. Whatever changes are made to BIOSYS, therefore, need to be mirrored in DARLEQ, else the software will not pick up all the data when it calculates indices.   Finally, whatever happens in England also needs to be done in Scotland, Wales and Northern Ireland, as the environment is a responsibility of the devolved administrations whilst the UK as a whole still presents a unified front to Brussels.

In theory, there is a single “hub”, the National Biodiversity Network, which links all names to a code which can then be used in databases across all organisations to link biological data with site and sample information. However, the NBN still needs to be fed information on changes to particular groups of organisms by specialists and this is where the system has broken down.   It is a problem that I have touched on before: there is no single authority for the diatoms who can arbitrate on additions or changes to the diatom flora of Britain and Ireland.   The tradition of biological recording, often underpinned by enthusiastic amateurs around the country, simply does not exist for this group (though it is worth remembering that the current, somewhat dated, checklist was the product of Bernard Hartley, an amateur).

I’m hoping that one of the functions of the Flora project team will be to act as the de facto “authority” that can feed changes to the NBN and, through them, to the environmental agencies and others who use diatoms. I would go further: the online Flora will not, actually, fulfil its ambition of reducing errors during ecological assessments unless there is a pathway through which these changes can be disseminated to the database managers who are the custodians for all the ecological information that has been collected over the past 25 years or so.

This, then, is the ecology of information in practice. Just as a pure ecologist wants to understand the structure of an ecosystem, and how all the parts relate to one another, so applied ecologists also need to be aware of how data and information (the “energy” in our bureaucratic ecosystems) gets from the field notebooks of scientists to the managers tasked with making decisions about environmental regulation. To push my analogy just a little further, small changes in biological nomenclature have the potential to make data unpalatable to the computer programs that “graze” on the results of our hard work. It should not be a big deal, if handled wisely, but budget cuts mean that this cannot always be taken for granted.

Reference

Hartley, B. (1986). A check-list of the freshwater, brackish and marine diatoms of the British Isles and adjoining coastal waters. Journal of the Marine Biological Association of the United Kingdom 66: 531-610.

Williams, D.M. (2011). Synedra, Ulnaria: definitions and descriptions – a partial resolution. Diatom Research 26: 149-153.

More than just an insignificant dot?

One of the more unusual habitats for freshwater algae that I’ve encountered recently is the surface of a “sonde” – a submersible instrument that measures water quality attributes (“sonde”, as far as I can tell, simply means “probe” in French, but seems to have slipped into general usage in the water quality monitoring fraternity).   Mel Lacan from Natural Resources Wales sent me some photographs of tiny colonies that she and a colleague had found on a sonde submerged in a small tributary of the lower Wye and photographed.   At first, I thought it was Heribaudiella fluviatilis, which forms similar dark-brown colonies and it took the eagle eyes of Dave John to spot that I had not just got the wrong genus, but the wrong phylum (Heribaudiella is one of just three representatives of the Phaeophyta, or brown algae, found in UK freshwaters.   These colonies are, in fact, formed from filaments of a Rhodophyta (red alga), probably Audouinella pygmaea.   We’ve seen another Audouinella species, A. hermanii, in the River Ehen (see “The schizophrenic life of red algae …” and references therein), but I had not seen this particular species before.   Whereas A. hermanii formed pink-tinged mats on the bed of a fast-flowing stream in winter, this population of A. pygmaea forms dark brown spots and was found just above the tidal limit in a tributary of the River Wye.

Audouinella_pyg_on_sonde

Colonies of Audouinella pygmaea on a sonde submerged in the Anghidi Fawr stream, May 2015 (The light brown objects are pupal cases of simuliidae flies). Scale bar: 1 centimetre. Photograph: Mel Lacan, Natural Resources Wales.

It is hard to be 100% sure about the identity of this population as it does not totally match the description in the Freshwater Algal Flora of the British Isles and, moreover, there are no reproductive organs present (so it could just be a “chantransia” stage – see comments in the earlier post). Some samples have been sent off to experts for their opinions.

Mel sent some of the colonies to Chris Carter and he has produced a series of spectacular photographs that illustrate the structure of these Audouinella colonies very clearly. The first pair show the linear, sparsely-branched filaments radiating out to form the hemispherical colonies that were growing on the sonde. The second pair shows the filaments at higher magnification and you can see the brownish-green colour of the cells very clearly. Along with chlorophyllsred algae contain phycobiliprotein pigments which lend the group their distinct colouration.   In most red algae, a red pigment called phycoerythrin dominates, giving the group their common name. However, a blue-colured variant called phycocyanin can also be abundant in some species, including A. pygmaea.   The description of A. pygmaea in the Flora refers to its blue-colour. Here, however, we have a brownish hue, presumably reflecting a mix of these two pigments along with the green chlorophyll. These accessory pigments helps red algae to make the most of the limited light available at great depths in the oceans.   It is probably also offers a competitive advantage to freshwater red algae, many of which are associated with shaded sections of streams.

Audouinella_-tuft-lomag2

A low-magnification view of an Audouinella pygmaea colony from the side (left) and from above (right).   Photograph: Chris Carter.

Audouinella_pyg_CCarter_May

Medium- and high-power views of Audouinella pygmaea filaments from the submerged sonde from Anghidi Fawr stream, May 2015. Photographs: Chris Carter.

The evidence that demonstrates conclusively that this is a red alga can be seen in the image below. A gap in the cell walls often remains between daughter cells after cell division, which means that the protoplasm of the two cells is connected.   As the cells develop, these “pit connections” become filled by “pit plugs”, formed from protein and polysaccharide, which are just visible in the light microscope.   Not all red algae have pit plugs, but it is particularly characteristic of the class Floridophyceae, to which Audouinella belongs.

Audouinella_pygmaea_pits

A high magnification view of filaments of Audouinella pygmaea from Anghidi Fawr stream, May 2015, with arrows indicating the pit connections between adjacent cells.

A few months ago, I wrote about the problems of knowing whether algae were genuinely rare or simply not very well recorded (see “A “red list” of endangered British diatoms?”). The Freshwater Algae Flora of the British Isles refers only to a single record of Audouinella pygmaea (River Deveron, Scotland), whilst my old copy of West and Fritsch also mentions a record at “Penyghent” in West Yorkshire.   Audouinella pygmaea is a good example of an alga that is probably under-recorded.   These tiny dark-brown spots are very easily overlooked by all but the most observant surveyors.   I suspect that it is more common than we think but that it is overlooked by both macrophyte surveyors (who are generally focussed on larger organisms) and diatom samplers (whose methods preclude the study of soft-bodied algae). A map of the current distribution of Audouinella pygmaea in the UK will, therefore, give an indication of where eagle-eyed surveyors are work than reveal any deep biogeographical truths.

Postscript: this post has been extensively re-written as closer observation by Dave John led us to change our initial conclusions about the identity of the alga. As Chris Carter pithily put it as we mulled over the issue, “anyone who does not make mistakes does not make anything”

References

John, D.M., Whitton, B.A. & Brock, A.J. (2011). The Freshwater Algal Flora of the British Isles. 2nd Edition. Cambridge University Press, Cambridge.

West, G.S. & Fritsch, F.E. (1927). A Treatise on the British Freshwater Algae.   Cambridge University Press, Cambridge.

 

Croft Kettle through the magnifying glass …

Croft_Kettle_150529_#3

Cymbella-dominated community of epiphytic algae around Chara hispida stems in Croft Kettle, May 2015.

The final stage of my journey of discovery through Croft Kettle is a three-dimensional diorama in which the various components that I have described in posts since my visit on 29 May are reassembled into something approaching their natural state.   In this image, I have tried to show how much of the yellow-brown gunk which you can see in my post of 1st June is, in fact, the stalks of Cymbella cymbiformis, which form a dense matrix around the Chara stems. This, in turn, creates a habitat within which other diatoms can move around. In my illustration, I have included cells of Navicula radiosa and Amphipleura pellucida as well as Rhopalodia gibba and several crystals of calcite. The Rhopalodia intrigues me: Chris Carter’s photographs in my post from 7 June show it attached to Chara stems but I did also see it moving around in samples dominated by the Cymbella stalks.   Adhering strictly to a sessile lifestyle when Cymbella stalks are growing all around you and creating a light-capturing canopy is probably not a great survival strategy and the capacity to move amidst this forest of stalks must give the Rhopalodia more opportunities.   On the other hand, Rhopalodia is not really optimised for motility, as both of it’s raphe slits are on the same side, in contrast to Navicula and relatives where they are on opposite sides. Diatoms exude mucilage through the raphe which attaches to the surface and then gives them something to push against. In this Cymbella forest, these stalks will, presumably, provide that point of contact.   As the diatom pushes against the stalk, it will need to connect with another stalk before it can progress. Having two raphe slits on opposite sides of the valve increases the chances of this happening (in much the same way as a climber using both arms and both legs to work his or her way up a narrow chimney). Having both on the same side, presumably, reduces the chance of successfully adhering to another stalk.   It is, I suspect, a case of “needs must”: limited motility is still better than no motility at all.   If you look carefully, you’ll see that I’ve also included some cyanelles in the Rhopalodia cells.

It is slightly disingenuous for me to suggest that this image is purely the result of my own observations.   They are, for sure, the starting point but I find myself referring to several books as I constructed the image. The view down the microscope has a very flattened perspective, which means that it can be difficult to get an impression of the three-dimensional appearance of a diatom such as Rhopalodia.   For this, I referred to scanning electron micrographs in The Diatoms: Biology and Morphology of the Genera. However, these show the diatom frustules as opaque so I then need to refer back to my own images in order to build up a view of the cell interior.   I can start from my own observations but, after a few days, the chloroplasts of some species start to degrade, so I also turned to Eileen Cox’s book on identification of live diatoms. This is good for details of the plastids, but not so good for stalks so, for these, I am back to peering down my microscope at fresh material.   Finally, I found an excellent new book on charophytes that had some great illustrations that helped me understand the structure of the stem of Chara.

This interplay between direct observation and existing knowledge is necessary and, indeed, there are noble precedents (see “I am only trying to teach you to see …”). However, it also carries the possibility that we promulgate the errors of the past; we look at the natural world through eyes conditioned by the opinions and interpretations of others.  But, then, my picture is no more than an accumulation of my own opinions and interpretations.   In science, as in history, we always walk backwards into the future …

References

Cox, E.J. (1996). Identification of Freshwater Diatoms from Live Material. Chapman & Hall, London.

Round, F.E., Crawford, D.M. & Mann, D.G. (1990). The Diatoms: Biology and Morphology of the Genera.   Cambridge University Press, Cambridge.

Urbaniak, J. & Gąbka, M. (2014). Polish Charophytes: An Illustrated Guide To Identification. Wroclaw University of Environmental and Life Sciences. Wroclaw.

Alice’s adventures in Croft Kettle …

I cannot leave the subject of Croft Kettle without mentioning one tangential association of this small pond with the world of literature.   Croft Kettle is just over a kilometre from the village of Croft-on-Tees, just south of Darlington and, in the middle of the 19th century, the rector of Croft was the Reverend Charles Dodgson.   His eldest son was also Charles Dodgson, better known by his pen-name Lewis Carroll.   Several writers have explored the ways in which north-east England fuelled his imagination and provided raw material for Alice in Wonderland and Alice’s Adventures Through The Looking Glass (most notably Bryan Talbot’s excellent Alice in Sunderland, 2007, Jonathan Cape, London). One of these, a geologist called Tony Cooper from the British Geological Survey, even brought Croft Kettle into the story.   Croft Kettle is a sinkhole, formed by the dissolution of gypsum (calcium sulphate) and there was a local legend that the pond was bottomless, leading Cooper to wonder whether this deep, deep hole in the ground so close to where he lived was an inspiration for the rabbit hole into which Alice fell and tumbled “down, down, down”. When Carroll was older, his father moved from Croft to become the Dean of Ripon, also in north-east England and another region where there were many sinkholes.   Some of these appeared quite suddenly, with catastrophic consequences for houses built in the vicinity and, intriguingly, Cooper notes that the original model for Tenniel’s illustration of Alice, lived in a house affected by such subsidence in Ripon.   Curiouser and curiouser, as Alice might have said.